On 1/02/2011 7:50 AM, Sai Pooja wrote:
I think I have figured out the reason. It is because I am carrying out
replica exchange (manual) after every mdrun. If the exchange occurs, I
exchange the checkpoint files, extend the simulation by 500 steps and
continue. The new simulation starts from exchanged cptfile. It seems
that whenever the exchange occurs, the earlier log,traj files are not
appended. They are instead overwritten. the obv solution is to save
and index these files with the relevant replicas everytime an exchange
occurs.
This would have been good to know earlier. If replica-exchange leads to
the ensemble of the .tpr not matching the ensemble of the .cpt, then
IIRC 4.5.3 mdrun will refuse to start from the .cpt, which means the
subsequent mdrun will start from the .tpr only. Certainly a
non-appending mdrun prints a warning (or error, I forget which) message
to the log file, but perhaps the use of -append (erroneously) doesn't do
that. Please have a look and see if that is the issue. There is an
environment variable that can be set to tell mdrun that you (think you)
know what you are doing mismatching .tpr and .cpt.
Mark
However, i have a more general question. Since mdrun still runs with
the exchanged checkpoint files and starts from the point where the
previous run ended, can I be assured that an exchange has been
affected - since tpr files correspond to the "replica-box" and cpi to
the most recent exchanged replicas?
Pooja
On Mon, Jan 31, 2011 at 2:33 PM, Sai Pooja <saipo...@gmail.com
<mailto:saipo...@gmail.com>> wrote:
I manually index checkpoint files after every mdrun. What troubles
me is the randomness with which -append fails/works.
For eg, I have a simulation which runs from 3ns, 1ps in 1 mdrun.
Now oddly enough, the logfile starts from 1184ps(in the end, I do
remember the one starting from 0 but that was overwritten it
seems) and the rest is appended uptil the 3000ps step. Why would
append work from 1184ps to 3000ps but not for the previous
ones?Could it have anything to do with the network/cluster? If
that is the case is it safer to create a new file everytime and
then concatenate them after say every 100ps?
Pooja
On Sat, Jan 29, 2011 at 6:52 PM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> wrote:
On 30/01/2011 10:39 AM, Sai Pooja wrote:
I would be happy to supply more information.. if someone
could please look into this.. otherwise I will have to switch
to storing every file and then just concatenating them which
seems like a rather roundabout way of doing it.
As I suggested a few emails ago, are you sure that -cpi file
exists? If your numerical suffixes are indexing restarts, then
unless you've done some manual copying that you haven't told
us about, it won't. Your filename scheme seems a bit contorted
- like you're trying to do the work that GROMACS 4.5.x will
just do for you if you let it.
Otherwise, you'll have to do some detective work with gmxcheck
on the -cpi to see what might be the issue.
In your case, an initial
mdrun -deffnm rex_3
(perhaps save some copies while you're experimenting) and
subsequently
tpbconv -extend <blah> -f rex_3 -o rex_3
mdrun -deffnm rex_3 -append
will work and be much simpler than whatever you're trying to
do with filenames :-)
Mark
On Fri, Jan 28, 2011 at 4:37 PM, Sai Pooja
<saipo...@gmail.com <mailto:saipo...@gmail.com>> wrote:
This is the command:
nbs submit -command
"(/usr/local/gromacs/4.5.1/bin/mdrun_mpi -s rex_3.tpr -e
rex_3 -c after_rex_3 -cpi restart3 -cpo restart3 -ap
pend -g rexlog3 -x rextraj3);" -nproc 1 -name
"GENHAM-DIHEDRAL-3" -mail start end
Pooja
On Fri, Jan 28, 2011 at 4:20 PM, Mark Abraham
<mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 29/01/2011 3:56 AM, Sai Pooja wrote:
Hi,
I am using tpbconv and mdrun to extend a
simulation. I use it with the append option but
the files still get overwritten or erased. Can
someone help me in this regard?
Pooja
Commands (in python)
cmd = '(%s/tpbconv -extend %f -s rex_%d.tpr -o
rex_%d.tpr)' %(GROMPATH,dtstep,i,i)
os.system(cmd)
time.sleep(1)
cmd = 'nbs submit -command "'
cmd += '(%s/mdrun_mpi -noh -noversion -s
rex_%d.tpr -e rex_%d -c after_rex_%d -cpi
restart%d -cpo restart%d -append -g rexlog%d -x
rextraj%d >/dev/null); ' %(GROMPATH,i,i,i,i,i,i,i)
cmd += '" '
cmd += '-nproc 1 '
cmd += '-name "GENHAM-DIHEDRAL-%d" '%(i)
cmd += '-mail start end '
cmd += '-elapsed_limit 16h >> rexid'
os.system(cmd)
More useful for diagnostic and record-preservation
purposes is to construct the cmd string and print it
to stdout (or something).
At the moment it is far from clear that your -cpi
file exists for the new run.
Mark
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